Giardia undergo antigenic variation. Cloned populations contain small numbers of Giardia with unique surface antigens and these can be selected for by exposing Giardia to cytotoxic MAbs which react with original major antigen. Antigens present in the original isolate are not present in subsequent progeny and later antigens are not present in the original isolate. The major antigen of the original WB isolate (170 Kd) and one of the newly detected surface antigen are cysteine containing compounds. The DNA of clones of the original isolate (parents) were compared to the DNA of populations which grew following exposure to cytotoxic MAb (progeny). Multiple bands were seen in Southern blots using part of the cloned 170 kd antigen as a probe. Most progeny differed from each other but parent-progeny pairs were the same. Although frequent rearrangements were seen in the area encoding for this varying antigen, the differences in the banding patterns did not correlate with the loss of the major antigen. The major antigen of the parent isolate is a 170 kd antigen. Part of this gene was sequenced and showed two tandem repeats (65 amino acids) and part of a third. The entire segment has 12% cysteine. A Giardia gene was identified which hybridized under non- stringent conditions to hsp-70 of Drosphila. Sequence analysis of a 2 kb fragment revealed an open reading frame but no similarity to hsp-70. The promotor region had the typical heat shock promotor. The chromosomes of Giardia were identified using pulse field electrophoresis. Five chromosomes were identified and a number of minor less brightly staining Giardia DNA containing bands. Isolates differ in the position of the major bands and the number and position of the minor bands. Clones of the same isolate differ in the position of the minor bands.